The main goal of this project is to provide a consistent methodology for locating putative functional domains in unannotated nucleic acid sequences. Studies are conducted in two directions: 1) Determine by computational experiments, function-associated sequence patterns in large collections of functionally equivalent sequences. 2) Design protocols that will help "translate" observed sequence patterns into discriminant functions usable for mapping. A software for mapping not only genes but also various kinds of non-coding regions resulted from these studies. Detailed methodological guidelines for finding putative functional domains from sequence data are now being worked out. Project No. Z01 CB 08395-02 LMMB has been converged with this project. The database of illegitimate recombination sites is currently analyzed for the occurrence of significant non-contiguous pattern. A routine to map illegitimate recombination regions in unannotated sequences is now in preparation.